YTTV blends on-demand and DVR. It can be confusing even though it's probably the best way to do it for simplicity. But it can make a difference quality-wise.
On an FX show for example, you might set your DVR to record all episodes. That DVR recording you can fast forward through commercials, but it's an actual recording of the broadcast. But you could also choose the same show in your library and see a "choose version" under the recording, meaning there's an on-demand version and your DVR recording. If you pick the on-demand one you might be subjected to forced commercials. Sometimes the quality is better though, since it's a digital stream and not a recording.
Depends on the channel, show, policies in the area, etc. It's kind of a mess but not sure how you can deal with it any better than YTTV does considering the DVR space is truly unlimited.